create_fastas: Table To FASTA

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/create_fastas.R

Description

Using the output table from the download script and the user built genus-marker name parameter file to take the downloaded data and place them into fasta files.

Usage

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create_fastas(
  data_file = NULL,
  input_file = NULL,
  output_folder = NULL,
  no_marker = FALSE,
  no_taxa = FALSE,
  no_seq = FALSE,
  name_issue = FALSE,
  taxa_digits = FALSE,
  taxa_punct = FALSE
)

Arguments

data_file

NULL prompts the user to indicate the location of the data file in the format of the auto_seq_download output, anything other than NULL then the string supplied will be used for the location; default NULL

input_file

NULL prompts the user to indicate the location of the input file used to select through point and click prompts, anything other than NULL then the string supplied will be used for the location; default NULL

output_folder

NULL prompts the user to indicate the location of the output file through point and click prompts, anything other than NULL then the string supplied will be used for the location; default NULL

no_marker

If set to TRUE then will include records filtered out due to no marker data. Default is FALSE to not include records with no marker data.

no_taxa

If set to TRUE then will include records filtered out due to no taxa data. Default is FALSE to not include records with no taxa data.

no_seq

If set to TRUE then will include records filtered out due to no sequence data. Default is FALSE to not include records with no sequence data.

name_issue

If set to TRUE then will include records filtered out due to genus and species names with more than two terms. Default is FALSE to not include records with taxonomic naming issues.

taxa_digits

If set to TRUE then will include records filtered out due to genus or species names containing digits. Default is FALSE to not include records with digits in the taxonomic naming.

taxa_punct

If set to TRUE then will include records filtered out due to the presence of punctuation in the genus or species names. Default is FALSE to not include records with punctuation in the taxonomic naming.

Details

Input: File with list of genera with the molecular markers names below the taxa. The information to create this parameters file can be obtained from A_Summary.txt file from the download script results. For further details please see the documentation.

Value

This script outputs a fasta file of sequences for each column in the submitted parameters file. These files are named with the genera of interest and the first marker name in the column of the parameters file. These files are located in the folder where the Total_tables.txt file is located.

Author(s)

Rekkab Singh Gill

References

<https://github.com/rgyoung6/MACER> Young RG, Gill R, Gillis D, Hanner RH (2021) Molecular Acquisition, Cleaning and Evaluation in R (MACER) - A tool to assemble molecular marker datasets from BOLD and GenBank. Biodiversity Data Journal 9: e71378. <https://doi.org/10.3897/BDJ.9.e71378>

See Also

create_fastas() align_to_ref() barcode_clean()

Examples

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## Not run: 
create_fastas()
create_fastas(no_marker = TRUE, no_taxa = TRUE)
create_fastas(no_seq  = TRUE, name_issue = TRUE)

## End(Not run)

MACER documentation built on Sept. 8, 2021, 5:07 p.m.